Variant report

Variant	rs2943755
Chromosome Location	chr3:120004384-120004385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:120003899-120004443	MCF-7	breast:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
2	POLR2A	chr3:120004072-120004557	SK-N-MC	brain:	n/a	n/a
3	MAX	chr3:120004006-120004420	H1-hESC	embryonic stem cell:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
4	TCF12	chr3:120003825-120004442	ECC-1	luminal epithelium:	n/a	n/a
5	CTCF	chr3:120004340-120004490	NHEK	skin:	n/a	n/a
6	MAX	chr3:120003672-120004472	ECC-1	luminal epithelium:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
7	MAX	chr3:120003914-120004416	SK-N-SH	brain:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
8	MAX	chr3:120003778-120004530	ECC-1	luminal epithelium:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
9	MAX	chr3:120003833-120004535	H1-hESC	embryonic stem cell:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
10	MAX	chr3:120003825-120004548	H1-hESC	embryonic stem cell:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
11	E2F6	chr3:120003835-120004482	H1-hESC	embryonic stem cell:	n/a	chr3:120004378-120004388 chr3:120004137-120004147 chr3:120004284-120004293 chr3:120004170-120004181
12	MAX	chr3:120004079-120004385	SK-N-SH	brain:	n/a	chr3:120004147-120004156
13	HMGN3	chr3:120004013-120004427	K562	blood:	n/a	n/a
14	ZBTB7A	chr3:120003792-120004551	ECC-1	luminal epithelium:	n/a	chr3:120004339-120004346
15	MAX	chr3:120003882-120004487	MCF-7	breast:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
16	MXI1	chr3:120003847-120004521	IMR90	lung:	n/a	n/a
17	JUND	chr3:120004319-120004471	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr3:120003878-120004515	A549	lung:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
19	FOXP2	chr3:120004149-120004515	SK-N-MC	brain:	n/a	n/a
20	ZBTB7A	chr3:120003643-120004523	ECC-1	luminal epithelium:	n/a	chr3:120004339-120004346
21	TBP	chr3:120003713-120004437	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:120004079-120004521	SK-N-MC	brain:	n/a	n/a
23	MAX	chr3:120003669-120004576	A549	lung:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
24	E2F6	chr3:120003431-120004663	H1-hESC	embryonic stem cell:	n/a	chr3:120004378-120004388 chr3:120004137-120004147 chr3:120004284-120004293 chr3:120004170-120004181
25	E2F6	chr3:120003750-120004588	A549	lung:	n/a	chr3:120004378-120004388 chr3:120004137-120004147 chr3:120004284-120004293 chr3:120004170-120004181

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120004257..120007006-chr3:120012021..120014996,2	MCF-7	breast:
2	chr3:120002820..120005702-chr3:120066388..120068289,2	MCF-7	breast:

Variant related genes	Relation type
GPR156	TF binding region
ENSG00000163428	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10049256	0.81[ASN][1000 genomes]
rs1085620	0.95[ASN][1000 genomes]
rs1085622	0.95[ASN][1000 genomes]
rs1085624	0.95[ASN][1000 genomes]
rs10934512	0.81[ASN][1000 genomes]
rs10934515	0.81[ASN][1000 genomes]
rs10934516	0.81[ASN][1000 genomes]
rs10934517	0.81[ASN][1000 genomes]
rs12152218	0.81[ASN][1000 genomes]
rs13314898	1.00[ASN][1000 genomes]
rs1352458	0.81[ASN][1000 genomes]
rs1388755	0.84[ASN][1000 genomes]
rs1488761	0.81[ASN][1000 genomes]
rs1488764	0.81[ASN][1000 genomes]
rs1492271	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1907681	0.81[ASN][1000 genomes]
rs2035671	0.81[ASN][1000 genomes]
rs2130000	0.81[ASN][1000 genomes]
rs2171598	0.81[ASN][1000 genomes]
rs2319541	0.81[ASN][1000 genomes]
rs2319542	0.81[ASN][1000 genomes]
rs2319543	0.81[ASN][1000 genomes]
rs2874023	0.81[ASN][1000 genomes]
rs2971211	1.00[ASN][1000 genomes]
rs2971213	0.95[ASN][1000 genomes]
rs4263318	0.95[ASN][1000 genomes]
rs4314205	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4676809	0.81[ASN][1000 genomes]
rs4676822	0.81[ASN][1000 genomes]
rs4676832	0.84[ASN][1000 genomes]
rs6438567	0.81[ASN][1000 genomes]
rs6764549	0.81[ASN][1000 genomes]
rs6772226	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6776122	0.81[ASN][1000 genomes]
rs6777971	0.84[ASN][1000 genomes]
rs6787458	0.84[ASN][1000 genomes]
rs6803611	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6805050	0.81[ASN][1000 genomes]
rs7637828	0.81[ASN][1000 genomes]
rs7641838	0.81[ASN][1000 genomes]
rs7642171	0.81[ASN][1000 genomes]
rs7653263	0.81[ASN][1000 genomes]
rs7653396	0.81[ASN][1000 genomes]
rs787185	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs787198	0.95[ASN][1000 genomes]
rs787211	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs796824	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs813697	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs814182	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs902790	0.81[ASN][1000 genomes]
rs902791	0.81[ASN][1000 genomes]
rs902792	0.81[ASN][1000 genomes]
rs902794	0.81[ASN][1000 genomes]
rs923726	0.81[ASN][1000 genomes]
rs923727	0.81[ASN][1000 genomes]
rs923728	0.81[ASN][1000 genomes]
rs9289142	0.81[ASN][1000 genomes]
rs9289143	0.81[ASN][1000 genomes]
rs979682	0.81[ASN][1000 genomes]
rs9811483	0.84[ASN][1000 genomes]
rs9813834	0.81[ASN][1000 genomes]
rs9841122	0.81[ASN][1000 genomes]
rs9842302	0.81[ASN][1000 genomes]
rs9853082	0.81[ASN][1000 genomes]
rs9857123	0.81[ASN][1000 genomes]
rs9858566	0.81[ASN][1000 genomes]
rs9868312	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120003000-120004600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:120003200-120004400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr3:120003200-120004400	Bivalent/Poised TSS	NHDF-Ad	bronchial
4	chr3:120003200-120004800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr3:120003400-120004400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr3:120003400-120004400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr3:120003400-120004400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
8	chr3:120003400-120004400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
9	chr3:120003400-120004400	Active TSS	Fetal Kidney	kidney
10	chr3:120003400-120004400	Enhancers	Lung	lung
11	chr3:120003400-120004400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
12	chr3:120003400-120004400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
13	chr3:120003400-120004400	Enhancers	Spleen	Spleen
14	chr3:120003400-120004600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr3:120003400-120004600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:120003400-120004600	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr3:120003400-120004600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr3:120003400-120004600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:120003400-120004600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:120003400-120004600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
21	chr3:120003400-120004600	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr3:120003400-120004600	Active TSS	Brain Substantia Nigra	brain
23	chr3:120003400-120004600	Active TSS	Colon Smooth Muscle	Colon
24	chr3:120003400-120004600	Active TSS	HSMM	muscle
25	chr3:120003400-120004600	Bivalent/Poised TSS	NHEK	skin
26	chr3:120003400-120004600	Bivalent/Poised TSS	Osteobl	bone
27	chr3:120003600-120004400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:120003600-120004400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
29	chr3:120003600-120004400	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:120003600-120004400	Bivalent Enhancer	Liver	Liver
31	chr3:120003600-120004400	Active TSS	Brain Angular Gyrus	brain
32	chr3:120003600-120004400	Active TSS	Fetal Brain Female	brain
33	chr3:120003600-120004400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
34	chr3:120003600-120004400	Bivalent/Poised TSS	Fetal Stomach	stomach
35	chr3:120003600-120004400	Bivalent/Poised TSS	Left Ventricle	heart
36	chr3:120003600-120004400	Bivalent/Poised TSS	Thymus	Thymus
37	chr3:120003600-120004400	Active TSS	A549	lung
38	chr3:120003600-120004400	Active TSS	HSMMtube	muscle
39	chr3:120003600-120004600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
40	chr3:120003600-120004600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
41	chr3:120003600-120004600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
42	chr3:120003600-120004600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
43	chr3:120003600-120004600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:120003600-120004600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:120003600-120004600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:120003600-120004600	Active TSS	Aorta	Aorta
47	chr3:120003600-120004600	Active TSS	Brain Anterior Caudate	brain
48	chr3:120003600-120004600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
49	chr3:120003600-120004600	Active TSS	Right Atrium	heart
50	chr3:120003600-120004600	Bivalent/Poised TSS	NHLF	lung

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